My God! A technical thread! Well done!!
Reprogramming the ECU is generally confined to remapping the fuel (& MAYBE ignition) maps, based mostly on throttle position and engine RPM.
The bike NEEDS the air intake sensor for an over-riding adjustment to fuelling - to maintain the programmed A/F ratios despite varying intake air temps... cold start, altitude, weather.....
With non-OEM intake filters, the IAT sensor should be set up somewhere very close to an air intake. People have simply zip-tied them to one air filter, others have modified a filter to insert the sensor, with a Ramair they put a hole in the baseplate for it.